Re: [gmx-users] g_sas on pdb files

On 6/18/13 7:41 AM, erin.cutts wrote: I'm trying to compare the hydrophobic surface generated from my trajectory with g_sas to a range of random coil .pdb files with my protein sequence, but I can't figure out how to make the structure+mass input that is required for g_sas from my pdb files i.e

[gmx-users] g_sas on pdb files

I'm trying to compare the hydrophobic surface generated from my trajectory with g_sas to a range of random coil .pdb files with my protein sequence, but I can't figure out how to make the structure+mass input that is required for g_sas from my pdb files i.e. in the manual "Structure+mass(db): tpr t

Re: [gmx-users] g_sas : Total surface area

I meant subset :) On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M wrote: > Sir, > > Oh! I was using sunset index numbers for both. I am sorry. I will try > that and see. First option as protein and next the subset. Thank you > very much. > > Kavya > > > > On Wed, Dec 12, 2012 at 8:16 PM, Justin Le

Re: [gmx-users] g_sas : Total surface area

Sir, Oh! I was using sunset index numbers for both. I am sorry. I will try that and see. First option as protein and next the subset. Thank you very much. Kavya On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul wrote: > > > On 12/12/12 9:37 AM, Kavyashree M wrote: > >> Thank you very much for yo

Re: [gmx-users] g_sas : Total surface area

On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i

Re: [gmx-users] g_sas : Total surface area

Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g

Re: [gmx-users] g_sas : Total surface area

Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham > On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M wrote: > > > Dear users, > > > > I was calculating solvent accessible surface area for a trajectory > > using g_sas

Re: [gmx-users] g_sas : Total surface area

On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M wrote: > Dear users, > > I was calculating solvent accessible surface area for a trajectory > using g_sas. I used an index file with 3 sets (A, B, C) of mutually > exclusive residues but summing up to 20 amino acids. Then using > g_sas calculated sas

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

Thank you justin With best wishes and regards, Rama David On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul wrote: > > > On 11/22/12 1:54 PM, rama david wrote: > >> Hi justin, >> Thank you for reply. >> As per your suggestion, >> The whole protein should always be the group fo

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

On 11/22/12 1:54 PM, rama david wrote: Hi justin, Thank you for reply. As per your suggestion, The whole protein should always be the group for the surface calculation. Whatever subset of those atoms (i.e. residues of interest) can be the output group. So as per your suggesti

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

Hi justin, Thank you for reply. As per your suggestion, The whole protein should always be the group for the surface calculation. Whatever subset of those atoms (i.e. residues of interest) can be the output group. So as per your suggestion I have to select the protein as my option

Re: [gmx-users] G_sas change in hydrophilic and hydrophobic surface area

On 11/22/12 2:36 AM, rama david wrote: Dear user , I simulate the two protein in random coil position, when they come close they form antiparallel beta sheet structure. I want to calculate the change in hydrophilic and hydrophobic surface area over my simulation time. For usig g_sas Shou

Re: [gmx-users] g_sas doubt -reg

On 9/2/12 2:10 PM, venkatesh s wrote: Dear Sir / Madam, I want run Solvent accessible surface area in gromacs,i aware about g_sas is there but for selecting group little bit confusing Reading frame 0 time0.000 Select a group for calculation of surface and

[gmx-users] g_sas doubt -reg

Dear Sir / Madam, I want run Solvent accessible surface area in gromacs,i aware about g_sas is there but for selecting group little bit confusing Reading frame 0 time0.000 Select a group for calculation of surface and a group for output: Group 0 (

[gmx-users] g_sas

Hi Gromacs Users I want to plot SAS of residues with errobar. I want to know what is the meaning of third column in file of residue.xvg (output of g_sas)? which of the following expression is true about third column? 1) first answer=sqrt(summation(s_i - s_mean)/(N-1))) 2) second answer= first ans

Re: [gmx-users] g_sas; could not find a Van der Waals radius

afsaneh maleki wrote: Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for prot

[gmx-users] g_sas; could not find a Van der Waals radius

Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for protein and DOPC are ffg53a6 a

Re: [gmx-users] g_sas

afsaneh maleki wrote: Hi, Thanks dear Justin for useful reply, I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I sel

Re: [gmx-users] g_sas

Hi, Thanks dear Justin for useful reply, I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I select the whole system first

Re: [gmx-users] g_sas

afsaneh maleki wrote: Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In th

[gmx-users] g_sas

Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area p

[gmx-users] g_sas

Dear user, I have a system that is contained of protein-water-ions. There, I select the whole protein first for calculation, and then this protein for output. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc In this way I can obtain A

Re: [gmx-users] g_sas vdwradii.dat

On 31/12/2011 5:04 PM, afsaneh maleki wrote: Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. W

[gmx-users] g_sas vdwradii.dat

Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following wa

[gmx-users] g_sas of ligands

Dear Gromacs Users, I am calculating SAS using g_sas of ligands in my system: protein, 30 ligands in water. The hydrophobic SAS of ligands decrease and reach stable value. Hydrophilic remains stable over the simulation time. I am wondering whether it (the decrease o hydrophobic) is because of bin

[gmx-users] g_sas of ligands

Dear Gromacs Users, I am calculating SAS using g_sas of ligands in my system: protein, 30 ligands in water. The hydrophobic SAS of ligands decrease and reach stable value. Hydrophilic remains stable over the simulation time. I am wondering whether it (the decrease o hydrophobic) is because of bin

[gmx-users] g_sas

Dear All, I am wondering what kind of volume computed by g_sas? volume inside SAS or inside contact surface (Connoly volume)? Best regards, Thanks Nikolai -- - Dr. Nikolai Smolin Postdoctora

Re: [gmx-users] g_sas calculation

Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a gro

Re: [gmx-users] g_sas calculation

ahmet yıldırım wrote: Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surfa

Re: [gmx-users] g_sas calculation

Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output

Re: [gmx-users] g_sas calculation

ahmet yıldırım wrote: Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (prote

[gmx-users] g_sas calculation

Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group:

Re: [gmx-users] g_sas index files/hydrogen bonds

On 14/06/11, "Marzinek, Jan" wrote: > > > > > > > > > > > > > > > Dear Gromacs Users, > > >   > > > I am calculating the hydrophobic interface area using g_sas between ligands > (their hydrophobic solvent accessible surface area (SASA) >95%) and > hydrophobic residues of coi

[gmx-users] g_sas index files/hydrogen bonds

Dear Gromacs Users, I am calculating the hydrophobic interface area using g_sas between ligands (their hydrophobic solvent accessible surface area (SASA) >95%) and hydrophobic residues of coiled coil fragment of protein (two helical strands) as follows: Protein SASA + ligand SASA - Protein&Liga

Re: [gmx-users] g_sas query

On 7/05/2011 7:04 PM, Anirban Ghosh wrote: Hello Tsjerk & Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group

Re: [gmx-users] g_sas query

Hello Tsjerk & Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group (Protein+Lipid+Ions) as the calculation group a

Re: [gmx-users] g_sas query

On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Only you know where your ions are, and whether their contribution to surface area means anything. Make the hybrid groups accor

Re: [gmx-users] g_sas query

Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar wrote: > Hey Anirban, > > I would consider the ions part of the solvent. But the procedure is right. > >

Re: [gmx-users] g_sas query

Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, "Anirban Ghosh" wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I ne

[gmx-users] g_sas query

Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculatio

Re: [gmx-users] g_sas values for peptide in water and in DPC micelle

sa wrote: Dear all, Firstly, I wish you a happy new year filled with joy, health and lots of finding !! Now my question: I have simulated one peptide (25 AA length + N- and C- caps) in two environment: one in bulk water TIP3P water (A) and one with a DPC micelle in water (B). My pepti

[gmx-users] g_sas values for peptide in water and in DPC micelle

Dear all, Firstly, I wish you a happy new year filled with joy, health and lots of finding !! Now my question: I have simulated one peptide (25 AA length + N- and C- caps) in two environment: one in bulk water TIP3P water (A) and one with a DPC micelle in water (B). My peptide keep in the

[gmx-users] g_sas and g_rdf

Hi everyone, I'm trying to look at the radial distribution function of water around the surface of my protein. For that, I calculated the surface area per residue (g_sas -or). Since I didn't find in the litterature any criteria to choose a minimum area value to count a residue as a a surface resid

Re: [gmx-users] g_sas resarea.xvg

On 4/11/2010 11:04 PM, Justin A. Lemkul wrote: Carla Jamous wrote: Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R

Re: [gmx-users] g_sas resarea.xvg

Carla Jamous wrote: Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @

[gmx-users] g_sas resarea.xvg

Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title "Area per residue

Re: [gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi, >> the interface is now A + B - AB" >> WHy not HALF of (A+B-AB)  ? > > You are right. A + B - AB gives the Buried Surface Area, which is the amount of surface that gets excluded from the solvent by complexation (and consequently is twice the size of the interface). :) Tsjerk -- Tsjerk A.

Re: [gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

On 2010-08-26 21.58, Chih-Ying Lin wrote: Hi Execute g_sas to get protein interface From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? You are right. Thank you Lin -- David van d

Re: [gmx-users] g_sas => calculate the SASA for each residues ?

Chih-Ying Lin wrote: Hi How can I calculate the SASA for each residue ? From Manual => "The program will ask for a group for the surface calculation and a group for the output." When I issue the command => g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg => Gromacs will p

[gmx-users] g_sas => calculate the SASA for each residues ?

Hi How can I calculate the SASA for each residue ? >From Manual => "The program will ask for a group for the surface calculation and a group for the output." When I issue the command => g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg => Gromacs will pick Residue1.ndx as both a grou

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] g_sas for martini coarse-grained particles

also an example of the use of SASA is in JACS-2007, 129, 10126-10132 On Jul 18, 2010, at 1:59 AM, Sanku M wrote: Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe th

Re: [gmx-users] g_sas for martini coarse-grained particles

the vdW radius of Martini particues is 0.263 nm, or 0.526 nm for the diameter. This is clearly indicated in all the martini papers :)) On Jul 18, 2010, at 1:59 AM, Sanku M wrote: Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC l

[gmx-users] g_sas for martini coarse-grained particles

Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are united

Re: [gmx-users] g_sas

shahid nayeem wrote: Dear All Using g_sas on trajectory file with command g_sas -f .xtc -s .tpr -oa atomarea.xvg gives following output @title "Area per atom" @xaxis label "Atom #" @yaxis label "Area (nm\S2\N)" @TYPE xy 1 0.139885 0.0351154

[gmx-users] g_sas

Dear All Using g_sas on trajectory file with command g_sas -f .xtc -s .tpr -oa atomarea.xvg gives following output @title "Area per atom" @xaxis label "Atom #" @yaxis label "Area (nm\S2\N)" @TYPE xy 1 0.139885 0.0351154 2 0.0510893 0.0236223 3 0.0510077 0.0234374 4 0.051

[gmx-users] g_sas command with the -q option

Hi all, I have a system which is composed of hexane-peptide-water-peptide-hexane layers. There, I selected the hexane+peptide system as the calculation group, and the hexane group as the output group to calculate the hexane area that is in contact with water. To do this I used the g_sas command wi

[gmx-users] g_sas to calculate the n-hexane/water interface surface area

Hi all, I have a question regarding the g_sas command. Let's say I have an n-hexane/water interface. I want to calculate the accessible area between these two media. If I were to choose the calculation group as the 'system', and the output group as 'hexane' then, it should give me that area? Rega

Re: [gmx-users] g_sas -pbc ???

On 10/04/2010 2:35 PM, Chih-Ying Lin wrote: Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? By recognizing that surfaces can cross periodic boundaries. Take trjconv an example, I have tried trjconv

[gmx-users] g_sas -pbc ???

Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom... ) or, trjconv -center . I could not get what i wanted. Thank you Lin -- gmx

Re: [gmx-users] g_sas => protein and ligand aggregate interface area ?

Hey Lin, > Is it the same step as calculation of protein A and B interface, which David > mentioned above? > But replacing protein B to Ligand aggregate (small micelle of ligand) ? > g_sas -n ligand-micelle-index.ndx ? Of course. > Is my idea correct? Is it necessary to always question

[gmx-users] g_sas => protein and ligand aggregate interface area ?

HI As David said, => How to compute protein-protein interface area? "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" I want to calculate protein and ligand aggregate (small micelle of ligand) interface area. Is it the same step as calcu

[gmx-users] g_sas => micelle ?

HI how to calculate SASA of micelle using g_sas? i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the atom numbers of micelle. if micelle is not compact enough but there are no water molecules inside the micelle, will g_sas calculate the vacancy part inside the micelle? Or,

Re: [gmx-users] g_sas

On 2010-04-05 02.35, Chih-Ying Lin wrote: Hi From David, "If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas." => therefore, if i select a

[gmx-users] g_sas

Hi >From David, "If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas." => therefore, if i select a group consisting of a single residue, which is

[gmx-users] g_sas

Hi g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. I chose => protein for calculation group => protein for output group what does it define "hydrophobic solvent accessible surface area"? => does that, the surface area, enclose the hydrophobic atoms/

Re: [gmx-users] g_sas

On 2010-04-04 07.13, Chih-Ying Lin wrote: HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "To

[gmx-users] g_sas

HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "Total" @ s3 legend "D Gsolv" What does "Hydrop

Re: [gmx-users] g_sas

On 4/3/10 8:36 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Please consult the documentation. From g_s

Re: [gmx-users] g_sas

Chih-Ying Lin wrote: Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Please consult the documentation. From g_sas -h: "The program will ask for a grou

[gmx-users] g_sas

Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

Re: [gmx-users] g_sas

On 1/03/2010 6:29 PM, pawan raghav wrote: /I executed the following command. // //g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg /// // /xmgrace -nxy mdrun.xvg/ /I get two sets of values: one is bigger (black) than the other (red). /// /I have checked the manual and other sources, but I could not

Re: [gmx-users] g_sas

Hi Pawan, The legends are contained in the .xvg file. Try viewing the file. Cheers, Tsjerk On Mon, Mar 1, 2010 at 8:29 AM, pawan raghav wrote: > I executed the following command. > > g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg > > xmgrace -nxy mdrun.xvg > > I get two sets of values: one is b

[gmx-users] g_sas

*I executed the following command. ** **g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg *** ** *xmgrace -nxy mdrun.xvg* *I get two sets of values: one is bigger (black) than the other (red). *** *I have checked the manual and other sources, but I could not find an **answer about the black and red li

Re: [gmx-users] g_sas with pbc

andrea carotti wrote: Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using

[gmx-users] g_sas with pbc

Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f

[gmx-users] g_sas

Hi Gromacs user, I need to calculate solvent accessible area for some water molecules. I am wondering if g_sas can do it correctly. Do I need just define surface group as : protein + water molecule? Thanks, Nikolai. ___ gmx-users mailing listgmx-use

RE: [gmx-users] g_sas

...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: Friday, April 24, 2009 1:30 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] g_sas Hi, Of course you can. But if part of Protein A is buried in an interface, doing the SAS calculation over A only will also include the

Re: [gmx-users] g_sas

age- From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: >> Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re: >> [gmx-users] g_sas >> >> >> >> Cheong Wee Loong, Daniel

Re: [gmx-users] g_sas

Cheong Wee Loong, Daniel wrote: Thanks for the explanation. It is much clearer now. Although I still don't quite understand why we can't just use Protein A as the calculation group AND output group to find the SASA of protein A. If A is complexed to B in solvent you might want the true SASA o

RE: [gmx-users] g_sas

Ah ok. Fair enough. Thanks! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Friday, April 24, 2009 10:48 AM To: Gromacs Users' List Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel

Re: [gmx-users] g_sas

nces that g_sas asks you to read and cite. -Justin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re: [gmx-users] g_sas Cheong Wee

RE: [gmx-users] g_sas

...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote: > Thanks Justin for the reply. I did read the help and manual and understand > that the output file can b

Re: [gmx-users] g_sas

w the user flexibility and versatility. -Justin Thanks. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sas

RE: [gmx-users] g_sas

ssion list for GROMACS users Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote: > Dear all, > > > > I am interested to calculate the hydrophobic and hydrophilic area of the > surface of the protein layer I am simulating. It looked like g_sas > would be able to give

Re: [gmx-users] g_sas

Cheong Wee Loong, Daniel wrote: Dear all, I am interested to calculate the hydrophobic and hydrophilic area of the surface of the protein layer I am simulating. It looked like g_sas would be able to give me what I was looking for. But I was wondering what the difference is between the

[gmx-users] g_sas

Dear all, I am interested to calculate the hydrophobic and hydrophilic area of the surface of the protein layer I am simulating. It looked like g_sas would be able to give me what I was looking for. But I was wondering what the difference is between the calculation group and the output group.

Re: [gmx-users] g_sas, what's it all about?

Michel Cuendet wrote: Hi list, I wanted to post something about g_sas some time ago already, but didn't find time to. Here is the occasion. I believe g_sas does not actually compute the solvent accessible surface area (SASA, defined as the locus of the center of the probe sphere), but rath

Re: [gmx-users] g_sas, what's it all about?

Hi list, I wanted to post something about g_sas some time ago already, but didn't find time to. Here is the occasion. I believe g_sas does not actually compute the solvent accessible surface area (SASA, defined as the locus of the center of the probe sphere), but rather the molecular surfac

Re: [gmx-users] g_sas, what's it all about?

Peyman Yamin wrote: On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: Peyman Yamin wrote: On Wednesday 30 July 2008 12:58, David van der Spoel wrote: Peyman Yamin wrote: > Hello List! > > > > I use g_sas to calculate the solvent accessible surface area of some > > amphiphiles.

Re: [gmx-users] g_sas, what's it all about?

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > >> Peyman Yamin wrote: > >> > Hello List! > >> > > >> > > >> > > >> > I use g_sas to calculate the solvent accessible surface area of some > >> > >

Re: [gmx-users] g_sas, what's it all about?

Peyman Yamin wrote: On Wednesday 30 July 2008 12:58, David van der Spoel wrote: Peyman Yamin wrote: > Hello List! > > I use g_sas to calculate the solvent accessible surface area of some > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if > the hyd

Re: [gmx-users] g_sas, what's it all about?

On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > Peyman Yamin wrote: > > Hello List! > > > > I use g_sas to calculate the solvent accessible surface area of some > > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if > > the hydrophilic part is somehow not recogn

Re: [gmx-users] g_sas, what's it all about?

Peyman Yamin wrote: Hello List! I use g_sas to calculate the solvent accessible surface area of some amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the hydrophilic part is somehow not recognized, or these terms mean different things in g_sas context? For Triton, for

[gmx-users] g_sas, what's it all about?

Hello List! I use g_sas to calculate the solvent accessible surface area of some amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if the hydrophilic part is somehow not recognized, or these terms mean different things in g_sas context? For Triton, for instance, a big surfa

Re: [gmx-users] g_sas Vdwradii.dat

maite lopez cabezas wrote: Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité

Re: [gmx-users] g_sas Vdwradii.dat

Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité On Sat, Jun 7, 2008 at 4:50 PM, Dav

Re: [gmx-users] g_sas Vdwradii.dat

Xavier Periole wrote: On Sat, 07 Jun 2008 22:32:29 +0200 "Xavier Periole" <[EMAIL PROTECTED]> wrote: On Sat, 7 Jun 2008 15:04:34 -0400 "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a V

Re: [gmx-users] g_sas Vdwradii.dat

On Sat, 07 Jun 2008 22:32:29 +0200 "Xavier Periole" <[EMAIL PROTECTED]> wrote: On Sat, 7 Jun 2008 15:04:34 -0400 "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 1

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